The CLC Main Workbench is able to analyze expression data produced on microarray platforms and high-throughput sequencing platforms (also known as Next-Generation Sequencing platforms). Note that the CLC Main Workbench is not able to calculate expression levels based on the raw sequence data. This analysis has to be performed with the CLC Genomics Workbench. The result of this analysis can be imported and further analyzed in the CLC Main Workbench.
The CLC Main Workbench provides tools for performing quality control of the data, transformation and normalization, statistical analysis to measure differential expression and annotation-based tests. A number of visualization tools such as volcano plots, MA plots, scatter plots, box plots, and heat maps are used to aid the interpretation of the results.
- Experimental design
- Working with tracks and experiments
- Transformation and normalization
- Quality control
- Statistical analysis - identifying differential expression
- Feature clustering
- Annotation tests
- General plots